The Karolinska Macaque database KIMDB (1.1)

This database incorporates IGHV, IGHJ and IGHD sequences from four subgroups of macaques, namely Indian and Chinese origin Rhesus macaques and Indonesian and Mauritian origin Cynomolgus macaques comprising 45 macaques in total.

All IGHV and IGHJ sequences in the database were identified using the germline inference tool IgDiscover, as described in Vázquez-Bernat et al. Immunity 2021, PMID: 33484642. In brief, two independent IgM libraries were sequenced for each of 45 macaques (27 rhesus macaques and 18 cynomolgus macaques), utilizing a 3' UMI introduced during cDNA synthesis followed by 5' multiplex set amplification. The study was performed using an updated version of IgDiscover and used the Cirelli et al. IGHV, IGHJ and IGHD sequences as the starting database during germline inference. The resulting combined database contains 1197 IGHV, 53 IGHD and 16 IGHJ alleles. Several alleles were present in both rhesus and cynomolgus macaques.


... Rhesus macaques

Phylogenetic analysis of IGHV alleles identified by IgDiscover in the 27 rhesus macaques (15 Indian origin and 12 Chinese origin). IGHV families are indicated by arcs in different colors and alleles identical to those reported in Cirelli et al. are shown in red dashed lines. The scale bar represents the expected number of nucleotide substitutions per site. A total of 761 IGHV alleles were identified in the 27 animals and the number of alleles in each IGHV family is indicated in the inserted table.

... Cynomolgus macaques

Phylogenetic analysis of IGHV alleles identified by IgDiscover in 18 cynomolgus macaques (12 Mauritian origin and 6 Indonesian origin). IGHV families are indicated by arcs in different colors and alleles identical to those present in the IMGT cynomolgus database (downloaded in May 2020) are shown in red dashed lines. The scale bar represents the expected number of nucleotide substitutions per site. A total of 615 IGHV alleles were identified in the 18 animals and the number of alleles in each IGHV family is indicated in the inserted table.

Changelog

Update to KIMDB 1.1
March 17, 2022, 2:14 p.m.

  • Removed 6 nucleotide 5’ end prefix from all alleles of IGHV3-100 as this was part of the leader
  • Removed 3’ RSS signal sequence from alleles of IGHD3-15, IGHD3-16 and IGHD3-18
  • Added 13 novel IGHV alleles from animal D20 (Library reads from ERR2856338): IGHV1-NL_1*01_S2608, IGHV2-NL_1*01_S0252, IGHV3-143*01_S8819, IGHV3-36*01_S4906, IGHV3-5*01_S6435, IGHV3-NL_1*01_S7175, IGHV3-NL_14*01_S0414, IGHV3-NL_18*01_S1419, IGHV4-149*01_S2329, IGHV4-174*02_S2437, IGHV4-NL_12*01_S2985, IGHV4-NL_27*01_S7628, IGHV4-NL_36*01_S0326
Initial release of KIMDB 1.0
Jan. 1, 2021, 3:12 p.m.

The database has been populated with the sequences from update manuscript